17-75869576-T-G

Variant names:

• chr17-75869576-T-G
• rs9894383

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.301 in 151,822 control chromosomes in the GnomAD database, including 9,591 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (9591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45639 AN: 151704 Hom.: 9545 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.298

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.301 AC: 45741 AN: 151822 Hom.: 9591 Cov.: 32 AF XY: 0.294 AC XY: 21806 AN XY: 74226

African (AFR) AF: 0.599 AC: 24707 AN: 41256

American (AMR) AF: 0.221 AC: 3369 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3472

East Asian (EAS) AF: 0.134 AC: 694 AN: 5166

South Asian (SAS) AF: 0.200 AC: 962 AN: 4810

European-Finnish (FIN) AF: 0.108 AC: 1145 AN: 10604

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13184 AN: 67940

Other (OTH) AF: 0.303 AC: 639 AN: 2106

Alfa AF: 0.204 Hom.: 3126

Bravo AF: 0.323

Asia WGS AF: 0.212 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		-0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9894383; hg19: chr17-73865657;